Dharshini Sree Jaikumar

India

Retrospective Evolutionary Analysis of Dengue Virus Isolates Circulating in India between 2012-2024 Reveals Functionally-Relevant Selection Hotspots

Dharshini Sree Jaikumar1, Yuvashree Veeramani1, Rekha Ravindran1, Sriram Kumar1,2

1. Department of Biotechnology, Rajalakshmi Engineering College, Chennai, India
2. Institute of Virology, University Hospital Münster, University of Münster, Germany

Abstract

Background

Dengue virus, the pre-dominant arbovirus in India, causes recurrent epidemics with significant health burden; limited antiviral options and emerging resistance highlight the need to understand viral evolution. This study maps 14 years of Indian dengue strains to identify mutational patterns and functional hotspots, bridging key gaps in evolutionary insights.

Methods

We performed a retrospective evolutionary analysis of 2,500 high-quality, complete genomes from India (2012–2024) from GISAID. Using year-wise and multi-year alignments, we quantified amino-acid substitutions across all viral proteins. Consensus references were generated for each protein, and residue-wise frequency was calculated via custom Python pipelines, validated through entropy-based metrics. Functionally relevant hotspots were structurally mapped to assess their local effects.

Results

We identified mutational hotspots across all ten proteins, revealing a pattern in three critical proteins: Envelope, NS2B–NS3, and NS5. In Envelope, H52Q/L, V141I, I162V, and V322I map to Domain I, the glycan loop, and the EDIII–stem junction, tuning scaffold stability and loop exposure. H52Q remained stable, H52L was transient, and V322I re-emerged in 2024 after outbreak-year stabilization, indicating antigenic relevance. In NS2B, F21L and I59V/E63D in the cofactor region may modulate NS2B orientation and NS3 activation. In NS3, R15K and K73R affect surface protease regions, while K186R maps to the RTPase motif affecting RNA affinity. NS5 hotspots span the methyltransferase domain (A19S, K30R, V78M, K98R, I135T, A196T), influencing SAM binding and catalytic efficiency. Across all three proteins, hotspots were unstable in 2012–2021 but stabilized during outbreaks in 2022–2023.

Conclusions

Our analysis uncovers an active adaptive landscape in Indian dengue viruses, marked by structurally meaningful, temporally dynamic hotspots across key proteins. These insights refine our understanding of serotype-specific diversification and guide future antiviral, vaccine, and surveillance strategies.